Dear All,
I used unpacksdcmdir to unpack DTI data from Bay 3. The log file shows
"DTI is in non-moasic form, so cannot extract bvals/bvects"
My question is how to get bvals/bvects files from unpack?
The files look like:
42DIFFUSION_HighRes ok 128 128 62 1
MR.1.3.12.2.1107.5.2.32.35162.2
Dear All,
Does anyone know how to run regression (with covariates of interest) in
freesurfer. I know people usually do group comparison but I need to do
regression with a continuous variable. Or do I have to use SPM?
Cheers,
Jacky
___
Freesurfer mailin
Yes. Sorry, I should mention this: the data is DTI (FA maps) from FSL. Can
I still use the same methods?
> Hi Jacky, have you looked at the group analysis tutorial? It includes
> instructions on how to include age as a continuous covariate.
> doug
>
>
> On 12/12/2013 06:28 PM, r...@nmr.mgh.harvar
t; Bruce
> On Mon, 6 Feb 2017, Juhyoung Ryu wrote:
>
>>
>> Hi FS developers,
>>
>> I received errors in one of steps in recon-all.
>> I analyzed 111 individual subjects' T1 data using same method, but there are
>> errors in only 14 subjects.
>&
u tar and gzip the entire subject directory tree and upload that?
>
> thanks
> Bruce
>
> On Tue, 7 Feb 2017, Juhyoung Ryu wrote:
>
>> I uploaded 3 set of T1.nii and T2.nii files for 3 example subjects.
>> You can get subject information here : T1_CUBEE{#subject
g
recon-all.log
Description: Binary data
> On Feb 9, 2017, at 12:38 PM, Bruce Fischl wrote:
>
> sounds like you are using the old (5.2) recon-all. Are you sure it is 6 in
> your path?
>
> And can you email the list so others can answer?
>
> thanks
> Bruce
>
>
I checked version of recon-all script using 'recon-all -version’ command
and 'freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c’ is printed.
Juhyoung
> On Feb 9, 2017, at 1:02 PM, Bruce Fischl wrote:
>
> What does
>
> which recon-all
>
> return?
>
>> O
this kind of thing as text into your email
> instead of taking snapshots? That makes things easier for us.
>
> Second, why are you telling recon-all not to do the inflation with
> -noinflate2? That is why it can't find the inflated surface.
>
> cheers
> Bruce
>
>
Hi experts,
I'm trying to surface reconstruction using high-resolution T1 and T2 data
using freesurfer version 6
So I typed like this:
recon-all -subject ${subjName} -i T1_bfc.nii -hires -T2 T2_bfc.nii -T2pial
-all
and that excited with errors like this;
\n*
l -all -cw256
Thanks,
Juhyoung
> On Jul 28, 2017, at 2:19 AM, Bruce Fischl wrote:
>
> Hi Juhyoung
>
> what FS version are you running with? If 6.0 you want to include the -highres
> flag
>
> cheers
> Bruce
>
>
>
> On Thu, 27 Jul 2017, juhyoung Ryu wrot
suggestions to run freesurfer?
Thank you in advance!
Juhyoung
> On Jul 28, 2017, at 8:45 AM, Juhyoung Ryu wrote:
>
> Hi Bruce,
>
> Yes I’m using v6.0.
> I found that there is -hires flag in version 6
> (https://surfer.nmr.mgh.harvard.edu/fswiki
ng
>
> I think it's because you have -cw256. Since it comes after -hires it
> overrides it and tells recon-all to crop to a 256 volume size
>
> cheers
> Bruce
> On Fri, 4 Aug 2017, Juhyoung Ryu wrote:
>
>> Dear FS experts,
>> I want to reconstruct wh
k you so much,
Juhyoung
On Mon, Aug 7, 2017 at 11:18 PM, Bruce Fischl
wrote:
> Hi Juhyoung
>
> can you just cut and paste the text into the email instead of a screen
> shot?
>
> thanks
> Bruce
> On Mon, 7 Aug 2017, Juhyoung Ryu wrote:
>
> Sure, screenshot image is bel
> Begin forwarded message:
>
> From: juhyoung Ryu
> Subject: Re: [Freesurfer] recon-all error: ERROR! FOV=272.000 > 256
> Date: August 8, 2017 at 8:27:33 AM GMT+9
> To: Fr
>
> and change it to
>
> if (0 && $FOV_gt_256) then
>
>
>
> and re-run with the hires flag.
>
> Alternatively, you can reduce the FOV to 256 or less with mri_convert --crop
External Email - Use Caution
Hi all,
I’d like to upsampling anatomical ROI data, what i created using ribbon file,
to the functional resolution.
As the anatomical and functional data were aligned, I need only re-slice
processing except for coregistration.
I tried upsampling usi
eve, Douglas N.,Ph.D.
> wrote:
>
> Use bbregister to create the register.dat file. Run it with --help to
> get docs on how to use it.
>
> On 4/15/2019 7:51 AM, Juhyoung Ryu wrote:
>> External Email - Use Caution
>>
>> Hi all,
>>
>>
saparately to parallelize the processing. All script files
are located in the same diretory. Then I had the message as above. What
might be the problem? (It seems as if multiple terminal instances share the
socket port number)
2) How can I get interhemispheric distances between visual areas a
Regarding my first question in my previous post below,
the same error occurs even when I run my script (containing many repetition
of mris_pmake command) on only one terminal window.
From: Jungwon Ryu [mailto:rjung...@snu.ac.kr]
Sent: Tuesday, October 25, 2011 8:11 PM
To: 'frees
The other test commands for tkmedit (tkmedit test1 orig.mgz, tkmedit
test1 norm.mgz -segmentation mri/aseg.mgz ...) displayed the results
correctly.
If you could give me any suggestion what to do (without going back to
FC4 ... I have no control over it), it would be much appreciated.
Th
Hello Nick,
Thank you very much for your helpful suggestion. I will try it out and
report the results shortly.
Ryu
Nick Schmansky wrote:
Ryu,
I haven't encountered this error myself, nor do I have experience with
FC5, however, googling 'GLXBadLargeRequest' turns-up a
Dear all,
I am just writing to report that we are still having the problem I
reported before even after the the latest NVidia graphic driver was
installed. Our system administrators say that they cannot be certain
that it is really a driver problem.
Thank you,
Ryu Hashimoto
[EMAIL
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